Anna is almost certainly not a leader, if she was, it would be no use of her: we have seen her before using Gothielle (in the orphanage, tough it might`ve been changed for another mon), so that would mean she is a psychic type, in fact she was such in online league. We are already past Radomus. Also, you may check dev blog, some time ago field was released (starlight arena?) confirming Jirachi (4x boost and additional fire dmg for Doom Desire iirc, have fun without Flash Fire Houndoom). Probably we will battle Anna on that field. Anna is hinted too strong for a gym leader, and since we know who was a Champion, we know it has vacancy, the only option left is E4 member.
And for being missing: I think her doll is either real Jirachi, or gives her access to real Jirachi, and kids went to the mountains maybe to wake it up - I dont think we`ll meet them in the desert, they wandered east from the Agate, right in the direction of that rock climb path, also they are not part of Titania`s story.
My guess is, Meteor plotline still wont be resolved up until E4/Champion battle, they will be making their last stand there or league is corrupted and infiltrated by Meteor or so, and Champion/Final battle will be the Champion battle.